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              <center><font face="Helvetica, Futura, Arial"><font
 size="+2">FRM User Guide</font></font></center>
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  <td><font face="Helvetica, Futura, Arial">There are 3 tools in the FRM
set: frmr, frmv, and frm6. The first two perform a rotational matching between
a density map and an atomic structure (single molecule docking), whereas
the third does a full rigid body docking (fitting of an atomic structure
inside an EM map).</font></td>
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  <td valign="top"><a name="colores"></a><font
 face="Helvetica, Futura, Arial"><font size="+1">frmr &nbsp;and&nbsp; frmv
-&nbsp; FFT-accelerated 3D exhaustive rotational search</font></font>   
            
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Purpose:</font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif">These utilities
offer robust, accurate and fast rigid-body rotational search tools. The first
one, <b>frmr</b>, radializes the maps to be fitted, and thus is faster than
              <b>frmv</b>, which uses the full volumetric data. Both achieve
times of a few seconds, and it could be less than a second for <b>frmr</b>
if the maps are not too large.</font> </p>
               
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Usage (at shell prompt) (same for frmv):</font></font> <br>
 &nbsp; </p>
               
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  <td><tt>./frmr &lt;Situs density map&gt; &lt;PDB structure&gt; -res &lt;number&gt;
 -cutoff &lt;number&gt; -explor &lt;number&gt;</tt></td>
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              <p><font face="Helvetica, Arial, sans-serif">The input parameters
are:</font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>&lt;Situs density map&gt;</b> Low resolution map in Situs 
format.&nbsp;</font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>&lt;PDB structure&gt;</b> Atomic structure in PDB format.</font></font>
               </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-res&nbsp;</b> Estimated resolution of your density map
in &Aring;.&nbsp;<b> [default -res 15.0]</b></font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-cutoff</b>&nbsp; Density map cutoff value. All density
levels below this value are set to zero. </font></font><font
 face="Helvetica, Arial, sans-serif"><font color="#000000"><b>[default -cutoff
0.0]</b></font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b></b></font></font></p>
              <font face="Helvetica, Futura, Arial"><font
 color="#cc0000"></font></font>
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-explor</b>&nbsp; Controls the number of the best fits
to be output.<b> [default -explor 5]</b></font></font>                </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b><font size="+0"></font></b></font></font>&nbsp; </p>
               
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Input at program prompt:</font></font> <br>
               <font face="Helvetica, Futura, Arial"><font
 color="#000000">None.</font></font> <br>
 &nbsp; </p>
               
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Output:</font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif">The programs generate
a PDB file for each peak found. The files are named as follows:</font></p>
              <p><font face="Helvetica, Arial, sans-serif">frmr_best*.pdb
or frmv_best*.pdb,</font></p>
              <p><font face="Helvetica, Arial, sans-serif">where * signifies
numbers from 1 to the number of peaks found or the -explor option, whichever
is smaller.</font><br>
              <font face="Helvetica, Futura, Arial"></font></p>
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000"></font></font></p>
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  <td><font face="Helvetica, Futura, Arial"><font size="+1">frm6 -&nbsp;
FFT-accelerated 6D exhaustive search</font></font>                
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Purpose:</font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif">This is a rigid-body
rotational and translational search tool. It performs the fitting by recasting
the problem into a search of 5 angular and 1 linear parameters.</font> </p>
               
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Usage (at shell prompt):</font></font><br>
 &nbsp; </p>
               
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  <td><tt>./frm6 &lt;Situs density map&gt; &lt;PDB structure&gt; &lt;options&gt;</tt></td>
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              <p><font face="Helvetica, Arial, sans-serif">The input parameters
are:</font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>&lt;Situs density map&gt;</b> Low resolution map in Situs 
format.&nbsp;</font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>&lt;PDB structure&gt;</b> Atomic structure in PDB format.<br>
              </font></font></p>
               
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000">The &lt;options&gt; are:<br>
              <b><br>
-res </b>&lt;value&gt; &nbsp;Estimated resolution of your density map in
&Aring;.&nbsp;<b> [default -res 15.0]</b></font></font> </p>
                
              <p><font face="Helvetica,Arial, sans-serif">
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-ani </b>&lt;value&gt;<b><font size="+0">&nbsp;&nbsp;</font></b> 
Defines the resolution anisotropy factor (z direction vs. x,y plane)&nbsp;<b> 
[default: -ani 1.0]. </b></font></font><font
 face="Helvetica, Futura, Arial">Allows one to set a different resolution
in the z direction vs. the x,y plane. E.g. "-ani 1.5 -res 20" specifies a
30 A resolution in the z direction, and a 20 A resolution in x,y.</font> </p>
              </font><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-cutoff</b> &lt;value&gt; &nbsp;Density map cutoff value. 
All density levels below this value are set to zero. </font></font><font
 face="Helvetica, Arial, sans-serif"><font color="#000000"><b>[default -cutoff
0.0]</b></font></font> </p>
                
              <p><font face="Helvetica,Arial, sans-serif">
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b><font size="+0">-corr </font></b>&lt;number&gt;&nbsp;
This option controls whether the maps are pre-filtered with a Laplacian kernel.</font></font><br>
              <font face="Helvetica, Arial, sans-serif"><font
 color="#000000">Two values can be given here:</font></font> </p>
              <ul>
                <ul>
                  <font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-corr 0</b> Standard linear cross-correlation.&nbsp;
The scalar product between the density maps of the low resolution map and
the low-pass filtered atomic structure. For resolutions &gt; 10&Aring; this
criterion is less discriminative.</font></font>
                  <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-corr 1 [default]</b> A Laplacian filter is first applied
to maximize the fitting contrast. This is the default and is the recommended
docking criterion for low resolution docking (up to 25&Aring; resolution).
                  </font></font><font face="Helvetica, Futura, Arial">To provide
for a more robust algorithm when dealing with cropped experimental data we
implemented a mask that filters out hard artificial surfaces. This is done
transparently for the user.</font></p>
                </ul>
              </ul>
  </font><font face="Helvetica,Arial, sans-serif">  </font><font
 face="Helvetica,Arial, sans-serif">
              <ul>
                <ul>
                  <p><font face="Helvetica,Arial, sans-serif">
                  <p></p>
                  </font></p>
                </ul>
              </ul>
              </font></p>
              <font face="Helvetica,Arial, sans-serif">
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b><font size="+0">-mode </font></b>&lt;number&gt;&nbsp;
This option controls the scanning of the linear parameter (rho)</font></font>.<br>
              <font face="Helvetica, Arial, sans-serif"><font
 color="#000000">Three values can be given for this option:&nbsp;</font></font> 
              </p>
              <ul>
                <ul>
                  <font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-mode 0 [default]</b> &nbsp;Automatically select rho
scanning mode 1 or 2. This is done according to the relative sizes and shapes
of the molecules.</font></font>
                  <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-mode 1</b> &nbsp;Determine an initial value of rho and
start the search </font></font>from there.<br>
 </p>
                  <p><font face="Helvetica,Arial, sans-serif">
                  <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-mode 2</b> &nbsp;Scan the whole range of</font></font>
rho.</p>
                  </font></p>
                </ul>
              </ul>
              </font>
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b>-explor</b> &lt;number&gt; &nbsp;Controls the number
of the best fits to be output.<b> [default -explor 5]</b></font></font>  
             </p>
               
              <p><font face="Helvetica,Arial, sans-serif">
              <p><font face="Helvetica, Arial, sans-serif"><font
 color="#000000"><b><font size="+0"></font></b></font></font></p>
              </font> </p>
               
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Input at program prompt:</font></font> <br>
               <font face="Helvetica, Futura, Arial"><font
 color="#000000">None.</font></font> <br>
 &nbsp; </p>
               
              <p><font face="Helvetica, Futura, Arial"><font
 color="#cc0000">Output:</font></font> </p>
               
              <p><font face="Helvetica, Arial, sans-serif">This program generates
a PDB file for each peak found. The files are named as follows:</font></p>
 
              <p><font face="Helvetica, Arial, sans-serif">frm6_vol_best*.pdb
&nbsp;or&nbsp; frm6_lap_best*.pdb,<br>
              </font></p>
              <p><font face="Helvetica, Arial, sans-serif">according to whether
the <b>-corr</b> option is 0 or 1, and where * signifies numbers from 1 to
number of peaks found or the -explor option, whichever is smaller.</font><br>
                                                                        
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